DNA Binding and Cleavage, Stopped-Flow Kinetic, Mechanistic, and Molecular Docking Studies of Cationic Ruthenium(II) Nitrosyl Complexes Containing “NS4” Core

Abstract

This work aimed to evaluate in vitro DNA binding mechanistically of cationic nitrosyl ruthenium complex [RuNOTSP]+ and its ligand (TSPH2) in detail, correlate the findings with cleavage activity, and draw conclusions about the impact of the metal center. Theoretical studies were performed for [RuNOTSP]+, TSPH2, and its anion TSP−2 using DFT/B3LYP theory to calculate optimized energy, binding energy, and chemical reactivity. Since nearly all medications function by attaching to a particular protein or DNA, the in vitro calf thymus DNA (ctDNA) binding studies of [RuNOTSP]+ and TSPH2 with ctDNA were examined mechanistically using a variety of biophysical techniques. Fluorescence experiments showed that both compounds effectively bind to ctDNA through intercalative/electrostatic interactions via the DNA helix’s phosphate backbone. The intrinsic binding constants (Kb), (2.4 ± 0.2) × 105 M−1 ([RuNOTSP]+) and (1.9 ± 0.3) × 105 M−1 (TSPH2), as well as the enhancement dynamic constants (KD), (3.3 ± 0.3) × 104 M−1 ([RuNOTSP]+) and (2.6 ± 0.2) × 104 M−1 (TSPH2), reveal that [RuNOTSP]+ has a greater binding propensity for DNA compared to TSPH2. Stopped-flow investigations showed that both [RuNOTSP]+ and TSPH2 bind through two reversible steps: a fast second-order binding, followed by a slow first-order isomerization reaction via a static quenching mechanism. For the first and second steps of [RuNOTSP]+ and TSPH2, the detailed binding parameters were established. The total binding constants for [RuNOTSP]+ (Ka = 43.7 M−1, Kd = 2.3 × 10−2 M−1, ΔG0 = −36.6 kJ mol−1) and TSPH2 (Ka = 15.1 M−1, Kd = 66 × 10−2 M, ΔG0 = −19 kJ mol−1) revealed that the relative reactivity is approximately ([RuNOTSP]+)/(TSPH2) = 3/1. The significantly negative ΔG0 values are consistent with a spontaneous binding reaction to both [RuNOTSP]+ and TSPH2, with the former being very favorable. The findings showed that the Ru(II) center had an effect on the reaction rate but not on the mechanism and that the cationic [RuNOTSP]+ was a more highly effective DNA binder than the ligand TSPH2 via strong electrostatic interaction with the phosphate end of DNA. Because of its higher DNA binding affinity, cationic [RuNOTSP]+ demonstrated higher cleavage efficiency towards the minor groove of pBR322 DNA via the hydrolytic pathway than TSPH2, revealing the synergy effect of TSPH2 in the form of the complex. Furthermore, the mode of interaction of both compounds with ctDNA has also been supported by molecular docking.

Nano-crystallites of a ruthenium(iii) violurate complex: synthesis, characterization, PXRD and DFT structural analysis. DNA/HSA-binding, antiviral activity against COVID-19 and molecular docking study

“…These findings are consistent with the usual fact that the metal complex has a greater tendency to bind to biomolecules such as DNA and HSA than to its ligand. 34,35,73 The observed higher binding tendency of the Ru( iii ) complex can be attributed to the coordination of the nitrogenous bases of HSA with the Ru( iii ) center as previously mentioned in the case of DNA.…”

“…These results are similar to those reported for bis-(violurate)-based Mn( ii ) and Cu( ii ) complexes 34 and higher than reported for other ruthenium complexes. 35 In the same vein, the present Ru( iii ) complex binds to DNA via an intercalation mode similar to the known intercalator [Ru(L) 2 (dppz)]. 73 The lower k b value in the case of violuric acid compared to its Ru( iii ) complex indicates that the DNA binding affinity of the Ru( iii ) complex is higher than that of the violuric acid.…”

“…Many studies indicate that the anticancer activity of organic ligands and their transition metal complexes is related to their ability to bind to DNA. 34–41 In fact, the current study focuses on the same approach and thus seeks to find a relationship between the ability of violuric acid and its bis-(violurate)-based Ru( iii ) complex to bind to DNA and their anti-COVID-19 activity.…”

“…Ruthenium complexes are known to be effective therapeutic agents for many cancerous tissues, and their anticancer activity has been linked to their degree of binding to biomolecules such as DNA or HSA 35–41 In this regard, ruthenium complexes are distinguished from their platinum counterparts by their higher efficacy and lower toxicity, making them promising anti-cancer therapeutic agents. 42–45 In the same way, ruthenium complexes can have activity against viruses, specifically the corona virus, and therefore it is important to test ruthenium complexes as antiviral agents in the hope of obtaining a new therapeutic agent against SARS-CoV-2.…”

Hydroxychloroquine-Loaded Chitosan Nanoparticles Induce Anticancer Activity in A549 Lung Cancer Cells: Design, BSA Binding, Molecular Docking, Mechanistic, and Biological Evaluation

“…We used a stopped-flow technique for carrying out a kinetic investigation of the binding process because it is thought that DNA/protein–drug interaction is a fast step. This method aids in identifying the kinetic characteristics of the phases leading to intermediate species and ultimately obtaining an interaction mechanism [ 41 , 42 , 43 , 44 , 45 , 46 ], The geometrically optimized parameters (bond lengths, bond angles, and dihedral angles) were computed using DFT/B3LYP theory on the chitosan moiety and HCQ. Docking simulation will be used in order to confirm the spectroscopic results of the binding of HCQ to the BSA structure and the formation of the HCQ–BSA complex.…”